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university of cambridge  

   macroModel update

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemi cal Information Laboratory
and this information is for historical interest only

MacroModel Update

If you do not understand any of this DON'T PANIC. The default behaviour should allow you to ignore this with impunity.

To find out how much is queued on the different machines, type:
This will give you a list of everything on the queues, so you can log on to a machine which is not too busy.

The batchmin system for MacroModel has been updated, since severe slowdowns were being caused by multiple conformational searches being run simultaneously. By default, Monte Carlo conformational searches are now placed in a queue and performed consecutively rather than concurrently. ie If more than one Monte Carlo search is run, the second will not start until the first is completed, and so on.

Energy minimisations and other short calculations are unaffected by this change.

Several new hosts for running batchmin calculations have been set up. The host you should use depends on the type of calculation you are running.

To change your batchmin host, click on the 'Host' button in ENRGY Mode (it's on the left hand side, just above the 'Start' button). This will list the various hosts available. The currently available hosts are:

  • bmin45 (the default).

    This host runs all calculations interactively except for Monte Carlo conformational searches, which are placed in a queue as described above.

  • bmin45batch.

    This host places all jobs on the queue.

    You must use this host for molecular dynamics runs, dihedral drives, and any other calculation likely to last more than half an hour or so.

  • bmin1K, bmin2K, bmin5K, bmin5K750

    These hosts are for specialist use only, and should only be required for calculation on very large molcules. They should not be needed for general use.

So, for general use and conformational searching use bmin45, for longer calculations such as molecular dynamics use bmin45batch.

If you have any problems or bug reports concerning the new batchmin system please contact Mark Mackey or Jonathan Goodman .

© Goodman Group, 2005-2019; privacy; last updated January 19, 2019

department of chemistry University of Cambridge